[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms

[Dilip H N]

Hello,
I have a amino acid and i am using charmm 36 FF to create the topology by:-
 gmx pdb2gmx -f abc.pdb -o abc.gro....but i am getting error as:-

Atom HO in residue XXX was not found in rtp entry with xxx atoms while
sorting atoms.
So  if i use the -ignh flag in the gmx pdb2gmx command, i am getting the
topology and the .gro file, but i  in the .gro file the  the hydrogen in
the OH ie., in C terminal, is getting attached to N terminal (which was NH2
initially but in the .gro file it getting converted into NH3). So how do i
avoid the hydrogen getting shifted from OH or C terminal side to N terminal
side..??

How can i solve this error..??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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